Log in
HomeClass Notes1,200,000CA670,000

MIMM 214 Lecture 28: Generation of TCR Diversity & a Return to Antibodies

65 views7 pages
orangefrog35
12 May 2017
School
McGill University
Department
Microbiology & Immunology
Course
MIMM 214
Professor
Claire Trottier

For unlimited access to Class Notes, a Class+ subscription is required.

Document Summary

Generation of tcr diversity & a return to. You can also have diversity by pairing different & chains together. Have both combinatorial & junctional diversity for the tcr. Here you only remove what"s in the loop. The segments outside the loop (shown in the dotted lines) remain. Later that remaining v may do addition recombinations to allow for that small percentage of non-self reacting action. Constant generation of antigen-specific lymphocytes in the bone marrow. Most b cells in body die before they encounter their match; die by apoptosis in 4-5 days. You always have a very diverse array of antigen-specific lymphocytes in your body at any given time. 3 cdrs on , 3 cdrs on . Based on the diagram, cdr3 is the most responsible for antigen-binding; right in the center, so most variable region. After signal 1&2, need help from a t-cell to bind to mhc.

Get access

Grade+
$40 USD/m
Billed monthly
Grade+
Homework Help
Study Guides
Textbook Solutions
Class Notes
Textbook Notes
Booster Class
10 Verified Answers
Class+
$30 USD/m
Billed monthly
Class+
Homework Help
Study Guides
Textbook Solutions
Class Notes
Textbook Notes
Booster Class
7 Verified Answers

Related Documents

MIMM 214 Lecture Notes - Lecture 28: Rna Splicing, Plasma Cell, Immunoglobulin D
ivorykangaroo940
MIMM 214 Lecture Notes - Lecture 28: Pentamer, Immunoglobulin Class Switching, Somatic Hypermutation
graywolf744
MIMM 214 Lecture Notes - Lecture 17: Somatic Hypermutation, Immunoglobulin Class Switching, Alternative Splicing
whitechinchilla202

Related Questions

True / False Questions

01. _____ Antibody is composed of 2identical long heavy chains and 2 identical shorter lightchains.

02. _____ Variable (V) and constant(C) regions are part of both heavy and light chains.

03. _____ Variable regions for heavyand light chains from the same antibody molecule are alwaysidentical.

04. _____ Variable region of lightchains are encoded by the DNA sequences that contain rearranged V,D, and J segments.

05. _____ Fc part of the antibody isnot important, F(ab’)2 fragment has the same binding andeffector capacity.

06. _____ Fab fragments are generatedby alternative splicing.

07. _____ J chain is used as asurrogate light chain during pre-B cell receptor testing forsuccessful V(D)J rearrangement.

08. _____ Binding of the antigen byantibody is stabilized by disulfide bonds.

09. _____ RAG1/2 are always expressedin B cells at high level, because B cells need RAG1/2 to constantlyrearrange their V regions.

10. _____ “N” (non template)nucleotides are added by TdT.

11. _____ The 12/23 rule is appliedduring class switching.

12. _____ For B cells, V(D)Jrecombination occurs only in the bone marrow.

13. _____ The process of somatichypermutation helps to improve specificity of the antibody.

14. _____ In late pro-B cells, Vsegment is rearranged with DJ segments.

15. _____ Failure to eliminateself-reactive B cells may lead to serious autoimmune diseases.

16. _____ Mature, naïve B cellsexpress IgD and any of the other classes of antibody (IgM, IgG,IgA, or IgE) on their surfaces.

17. _____ B1 cells are present in theperitoneal cavity, pleural spaces and brain.

18. _____ AID (activation inducedcytidine deaminase) is expressed only in B cells and it canintroduce breaks in double stranded DNA.

19. _____ Different classes (isotypes)of antibodies have different effector functions, which aretriggered by special receptors expressed by a variety of cells.

20. _____ Plasma cells are terminallydifferentiated cells that produce large quantities ofantibodies.

21. _____ Repeated exposure to thesame antigen eventually leads to immunological exhaustion and lackof immunity, because there is no room for new plasma cells in thebone marrow.

22. _____ Germinal centers arespecialized sites within the bone marrow where Ig genes ofactivated B cells undergo affinity maturation.

23. _____ B cells can present antigensto T helper cells.

24. _____ Co-stimulatory molecules arerequired for efficient generation of memory B cells.

25. _____ Lymphocytes migrate to thelymphoid tissues in response to chemokines.

26. _____ Class switching duringgerminal center reaction is a random process.

27. _____ T cell independent responsescan generate strong and long lasting B cell memory.

28. _____ Fc receptors that arepresent on many different cell types are crucial for removal of thepathogens.

29. _____ The ideal vaccine should bedesigned to mimic the natural course of infection without causingsymptoms of the disease.

30. _____ The protective immunity canbe generated against any pathogen because there is virtuallyunlimited number of possible V regions, thus any antigen can berecognize by an antibody.

ou are studying a protein that you think consists of a heterodimer composed of a 30 kDa and a 40 kDa subunit, which are joined together by disulphide bonds. In addition to your protein sample you have available a SDS-PAGE gel, an electrophesis apparatus like the one you used in the laboratory, and a Bio-Rad Precision Protein Kaleidoscope standard (Bio-Rad catalogue number 161-0375). You also have access to two different sample buffers. Buffer A contains 4% (v/v) SDS and 5% (v/v) ß-mercapto ethanol. Buffer B contains 4% (v/v) SDS but no ß-mercapto ethanol. As per the practical, samples are heated at 95oC for 4 minues before they are loaded onto an SDS-PAGE gel and electrophoresed.

3a) Describe the experimental methods that would allow you to test your hypothesis. Provide sufficient detail such that an interested reader could faithfully repeat your experiment. In your answer describe the chemistry and biochemistry involved in your treatment. Must be less than 200 words HYPOTHESIS IS : ABOUT IF IT IS A GERODIMER AND COMPOSED OF DISULPHDIDE BONDS NOTE THERE IS NO DYE PRESENT SO HOW CAN I SEE THE RESULTS OF ELECTROPHORESIS WITHOUT? AND WITH THE MATERIALS LISTED ABOVE

NEED HELP PLEASE. CAN YOU PLEASE DO IT ALL NOT JUST ANSWER ONE.

MY ANIMALS ARE: HUMAN, KANGAROO, RHESUS MONKEY, BULLFROG, LAMPREY, SNAPPING TURTLE, TUNA, AND EARTHWORM

Step 3: Cytochrome c Analysis

Scientists have found that almost all living organisms have a gene that codes for a protein called Cytochrome c. This chart lists the amino acids found in the Cytochrome c protein of some of the organisms on your cladogram.

Note: not all the organisms you used will be in the chart; as such, you can focus this analysis on the animals that are in the chart. If you only chose three animals that are in the chart, you should probably extend your amino acid analysis to include a couple animals that aren’t on your cladogram.

You will use the data provided in this chart to compare and analyze the amino acid sequences for Cytochrome c among these organisms. Be sure that your comparison considers the entire amino acid sequence, through amino acid 112, and not just the first lines of the chart. Once you have compared the sequences, you will write a discussion about your findings.

Amino Acid Sequences in Cytochome-C Proteins

1-30

Amino Acid Position Number

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

Human, Chimpanzee

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

I

M

K

C

S

Q

C

H

T

V

E

K

Rhesus Monkey

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

I

M

K

C

S

Q

C

H

T

V

E

K

Horse

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Pig, Cow, Sheep

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Dog

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Gray Whale

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Rabbit

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Kangaroo

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Penguin

-

-

-

-

-

-

-

-

G

D

I

E

K

G

K

K

I

F

V

Q

K

C

S

O

C

H

T

V

E

K

Snapping Turtle

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

V

E

K

Bullfrog

-

-

-

-

-

-

-

-

G

D

V

E

K

G

K

K

I

F

V

Q

K

C

A

Q

C

H

T

C

E

K

Tuna

-

-

-

-

-

-

-

-

G

D

V

A

K

G

K

K

T

F

V

Q

K

C

A

Q

C

H

T

V

E

N

31-60

Amino Acid Position Number

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

55

56

57

58

59

60

Human, Chimpanzee

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

Y

S

Y

T

A

A

N

Rhesus Monkey

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

Y

S

Y

T

A

A

N

Horse

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

F

T

Y

T

D

A

N

Pig, Cow, Sheep

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

F

S

Y

T

D

A

N

Dog

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

P

G

F

S

Y

T

D

A

N

Gray Whale

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

V

G

F

S

Y

T

D

A

N

Rabbit

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

V

G

F

S

Y

T

D

A

N

Kangaroo

G

G

K

H

K

T

G

P

N

L

N

G

I

F

G

R

K

T

G

Q

A

P

G

F

T

Y

T

D

A

N

Penguin

G

G

K

H

K

T

G

P

N

L

H

G

I

F

G

R

K

T

G

Q

A

E

G

F

S

Y

T

D

A

N

Snapping Turtle

G

G

K

H

K

T

G

P

N

L

N

G

L

I

G

R

K

T

G

Q

A

E

G

F

S

Y

T

E

A

N

Rattlesnake

G

G

K

H

K

T

G

P

N

L

H

G

L

F

G

R

K

T

G

Q

A

V

G

Y

S

Y

T

A

A

N

Bullfrog

G

G

K

H

K

V

G

P

N

L

Y

G

L

I

G

R

K

T

G

Q

A

A

G

F

S

Y

T

D

A

N

Tuna

G

G

K

H

K

V

G

P

N

L

W

G

L

F

G

R

K

T

G

Q

A

E

G

Y

S

Y

T

D

A

N

61-90

Amino Acid Position Number

61

62

63

64

65

66

67

38

69

70

71

72

73

74

75

76

77

78

79

80

81

82

83

84

85

86

87

88

89

90

Human, Chimpanzee

K

N

K

G

I

I

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Rhesus Monkey

K

N

K

G

I

T

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Horse

K

N

K

G

I

T

W

K

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Pig, Cow, Sheep

K

N

K

G

I

T

W

G

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Dog

K

N

K

G

I

T

W

G

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Gray Whale

K

N

K

G

I

T

W

G

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Rabbit

K

N

K

G

I

T

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Kangaroo

K

N

K

G

I

I

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Penguin

K

N

K

G

I

T

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Snapping Turtle

K

N

K

G

I

T

W

G

E

E

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Rattlesnake

K

N

K

G

I

I

W

G

D

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

V

F

Bullfrog

K

N

K

G

I

T

W

G

E

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

Tuna

K

S

K

G

I

V

W

N

N

D

T

L

M

E

Y

L

E

N

P

K

K

Y

I

P

G

T

K

M

I

F

91-112

Amino Acid Position Number

91

92

93

94

95

96

97

98

99

100

101

102

103

104

105

106

107

108

109

110

111

112

Human, Chimpanzee

V

G

I

K

K

K

E

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Rhesus Monkey

V

G

I

K

K

K

E

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Horse

A

G

I

K

K

K

T

E

R

E

D

L

I

A

Y

L

K

K

A

T

N

E

Common Zebra

A

G

I

K

K

K

T

E

R

E

D

L

I

A

Y

L

K

K

A

T

N

E

Pig, Cow, Sheep

A

G

I

K

K

K

G

E

R

E

D

L

I

A

Y

L

K

K

A

T

N

E

Dog

A

G

I

K

K

T

G

E

R

A

D

L

I

A

Y

L

K

K

A

T

K

E

Gray Whale

A

G

I

K

K

K

G

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Rabbit

A

G

I

K

K

K

D

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Kangaroo

A

G

I

K

K

K

G

E

R

A

D

L

I

A

Y

L

K

K

A

T

N

E

Penguin

A

G

I

K

K

K

S

E

R

A

D

L

I

A

Y

L

K

D

A

T

S

K

Snapping Turtle

A

G

I

K

K

K

A

E

R

A

D

L

I

A

Y

L

K

D

A

T

S

K

Rattlesnake

T

G

L

K

K

K

K

E

R

T

D

L

I

A

Y

L

K

E

A

T

A

K

Bullfrog

A

G

I

K

K

K

G

E

R

Q

D

L

I

A

Y

L

K

S

A

C

S

K

Tuna

A

G

I

K

K

K

G

E

R

Q

D

L

V

A

Y

L

K

S

A

T

S

-

More information:

Cytochrome c is a protein used in cellular respiration by most eukaryotes, which is why it's a very common protein to use for comparisons. You don't need to know anything about cellular respiration or the protein itself to do this analysis; just remember that a protein is a specific chain of amino acids.

Which amino acids are found, and the order in which they're found (their sequence), determine the shape, structure, and function of the protein. Also remember that an amino acid sequence is directly determined by the DNA sequence, so similarities in one also indicate similarities in the other.

Please note that the entire sequence of 112 amino acids represents one protein, and this sequence data is all one chart, not four. As such, your analysis should consider the sequence as a whole, and not amino acids 1 – 30, then amino acids 31 – 60, etc.

Be careful not to read too much into the differences you find. Since this analysis only looks at one protein, you will not be able to connect differences here to specific differences in traits between organisms. In other words, it might be that all animals with a placenta have a “V” at a particular location, while animals without a placenta have either a “C” or a “K.” That similarity helps us confirm that those animals with a placenta are more closely related to each other than to the others, but the “V” does not code for the placenta, nor is it related to that particular trait at all.

How to Analyze the Data

While you analyze the data that you are given to identify similarities and differences, be sure to use specific data to draw your comparisons, hypotheses, and discussions from. It is especially helpful to quantitatively compare data. A good way to do this, or at least to start, is to pick one species as a starting point or ‘baseline’ and then compare the amount of differences between that and each other species. Be careful, though, about the conclusions you draw – if species B and C each have 5 differences from species A, then they could have anywhere from 0 to 10 differences with each other!

Once you’ve compared each animal to a baseline animal, you should also compare other pairs of species so that you can discuss their specific relationships. If you only have a few animals with data to analyze in part C, you could simply make this comparison for every pair. If you have 6 or 7 animals, then you could pick just a few pairs to compare.

There are other legitimate ways to form quantitative data – for instance, you could focus on specific locations where most animals have the same amino acid, but some are different. These types of analysis tend to be harder to interpret, though. If you choose to use them, I suggest that you still complete at least some of the above types of analysis as well.

The discussion topics that I'm looking for are:

Use the chart to compare the amino acid sequences for the organisms. Do this in a way that lets you obtain quantitative (numerical) data; see above for suggestions.

Hypothesize about how closely related the different organisms are, based on the amino acid data in the chart.

In particular, focus on organisms that are also found on your phylogenetic tree, but you may choose to discuss others, too. That would be especially helpful if you used only three or four of the organisms that are also in the chart, or if one or more organisms that you did not include in your tree jump out at you as being especially similar or especially different from the ones you did include.

This does not need to be in the form of a formal hypothesis; that is, you do not need to put this in “if/then/because” form.

Because “how closely related” can be interpreted in many ways, it’s often helpful to put this in relative terms: “Animal D is the closest relative to Animal A.” “Animals C and B are more closely related to each other than either one is to Animal D.”

Discuss how this analysis compares to the relationships that were shown on your phylogenetic tree.

To start, does the Cytochrome c data agree or disagree with the relationships shown on the tree?

Remember that "discuss" means more than simply identifying whether the relationships are the same or different as what is shown. You can also suggest why they're likely the same, or what possible differences could imply, if anything. See the note at the end of “More Information” above – don’t read TOO MUCH into any one piece of data!

If your amino acid analysis included animals that weren’t on your cladogram, you could use your amino acid data to speculate where they likely “fit” on the cladogram.

The phrase “common ancestor” should show up somewhere in this discussion.

Please be aware that Step 3 should be written as a short essay, not a list or set of questions and answers. You may include a chart or table for the quantitative data you identified, but the key findings should also be written in sentence form. Once you’ve finished writing this, please proofread for spelling, grammar, and writing clarity.

Step 3 should be a sizeable portion of this portfolio. I expect that your analysis should be about 250 – 400 words long in order to thoroughly analyze the data and discuss the questions.